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Yorodumi- PDB-2h77: Crystal structure of human TR alpha bound T3 in monoclinic space group -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h77 | |||||||||
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Title | Crystal structure of human TR alpha bound T3 in monoclinic space group | |||||||||
Components | THRA proteinThyroid hormone receptor alpha | |||||||||
Keywords | HORMONE/GROWTH FACTOR / TR alpha / T3 / HORMONE-GROWTH FACTOR COMPLEX | |||||||||
Function / homology | Function and homology information regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / female courtship behavior / negative regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of lipid catabolic process / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / regulation of thyroid hormone mediated signaling pathway / positive regulation of female receptivity / regulation of heart contraction ...regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / female courtship behavior / negative regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of lipid catabolic process / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / regulation of thyroid hormone mediated signaling pathway / positive regulation of female receptivity / regulation of heart contraction / cartilage condensation / type I pneumocyte differentiation / thyroid hormone binding / thyroid gland development / general transcription initiation factor binding / retinoic acid receptor signaling pathway / TBP-class protein binding / response to cold / hormone-mediated signaling pathway / ossification / erythrocyte differentiation / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of cold-induced thermogenesis / transcription by RNA polymerase II / cell differentiation / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | |||||||||
Authors | Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. ...Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, H.F.M. / Craievich, A.F. / Garrat, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function. Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. ...Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. / Garratt, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h77.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h77.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 2h77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/2h77 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/2h77 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30978.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THRA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6FH41, UniProt: P10827*PLUS |
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#2: Chemical | ChemComp-T3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.0 M sodium cacodylate and 0.1M sodium acetate threehydrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→62.994 Å / Num. all: 18468 / Num. obs: 18468 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 0.313 / Cor.coef. Fo:Fc: 0.753
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→32.22 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.588 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.207 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.043 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→32.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.39 Å / Total num. of bins used: 20
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